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wuyangf7 / OPERA

This software tool implements the OPERA (omics pleiotropic association) method to test for combinatorial pleiotropic associations of molecular phenotypes (e.g., expression level of a gene and DNA methylation level at CpG sites) with a complex trait of interest using summary-level data from GWAS and molecular QTL studies. OPERA is a Bayesian generalization of the SMR & HEIDI approach8 to a multi-omics model, where the molecular phenotypes are considered as exposures and only the complex trait is considered as the outcome. This tool can therefore be used to prioritize molecular phenotypes that mediate the genetic effects for complex trait and provide mechanistic interpretation of the GWAS signal.
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Two questions about OPERA #2

Closed cwnag-c closed 8 months ago

cwnag-c commented 8 months ago

Hello YangWu

Thank you for developing OPERA！

I had some questions about OPERA. First, i noticed that OPERA or SMR does not filter snps with ambiguous strand, could it influence the results? Second, i found some xQTL files were each chromosome separately，so can the stage 1 analysis be performed for each chromosome separately?

I am extremely grateful for your assistance in resolving this issue!

Thank you, ChaoWang

wuyangf7 commented 8 months ago

Hi Chao,

Thank you for your interest on our software tool!

Re 1) OPERA does not filter SNPs with ambiguous strand. But OPERA does comparison between the alleles in GWAS, xQTL and LD reference. So if a SNP has different allele information (e.g., strand) in three datasets, OPERA will remove such SNP.

Re 2) No, the stage 1 analysis requires the genome-wide input. But in stage 2 analysis, you can run the chromosome-wide analysis to accelerate the computation.

Hope it helps, Yang

cwnag-c commented 8 months ago

Do I need to filter out SNPs with ambiguous strand before I perform OPERA?

wuyangf7 commented 8 months ago

Yes, it is better to filter out SNPs with ambiguous strand before the analysis.

cwnag-c commented 8 months ago

Thank you so much for patiently answering my questions！！！